I would give it a little more time to make sure that the bottom and middle really are warmer than the top, but if it is, then I would remove the box and towel. Maybe you could lay a smaller piece of cloth on the wire to keep the egg from rolling.
You might also want to try placing your thermometer at different heights in the incubator because the top is usually warmer than the bottom, thats why you are supposed to put the thermometer on top of the eggs. I don't know how much of a tempature difference there would be around the emu egg, but you may want to check into it. Just place the theremometer on the wire mesh and write down the tempature and then raise the thermometer to however hiegh the emu egg is and see what tempature it says there. If the incubator has a fan, then it probably won't be a problem. It's just something you may want to check.